Strain identifier
BacDive ID: 17079
Type strain: 
Species: Thiothrix nivea
Strain Designation: JP2
Strain history: <- J.M. Larkin, JP2
NCBI tax ID(s): 870187 (strain), 1031 (species)
version 8.1 (current version)
General
@ref: 1955
BacDive-ID: 17079
DSM-Number: 5205
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Thiothrix nivea JP2 is a mesophilic, Gram-negative bacterium of the family Leucotrichaceae.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 870187 | strain |
| 1031 | species |
strain history
- @ref: 1955
- history: <- J.M. Larkin, JP2
doi: 10.13145/bacdive17079.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Leucotrichaceae
- genus: Thiothrix
- species: Thiothrix nivea
- full scientific name: Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Beggiatoa nivea
@ref: 1955
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Thiotrichaceae
genus: Thiothrix
species: Thiothrix nivea
full scientific name: Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 emend. Larkin and Shinabarger 1983
strain designation: JP2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.997
multimedia
- @ref: 66793
- multimedia content: EM_DSM_5205_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1955
- name: THIOTHRIX MEDIUM (DSMZ Medium 573)
- growth: yes
- link: https://mediadive.dsmz.de/medium/573
- composition: Name: THIOTHRIX MEDIUM (DSMZ Medium 573) Composition: Agar 12.0 g/l Na2S x 9 H2O 0.3 g/l NH4Cl 0.2 g/l Na-acetate 0.1 g/l K2HPO4 0.01 g/l MgSO4 x 7 H2O 0.01 g/l FeSO4 x 7 H2O 0.0035 g/l EDTA 0.001 g/l ZnSO4 x 7 H2O 5e-05 g/l H3BO3 5e-05 g/l MnSO4 x 4 H2O 1e-05 g/l Co(NO3)2 5e-06 g/l Na2MoO4 x 2 H2O 5e-06 g/l CuSO4 x 5 H2O 2.5e-08 g/l CaSO4 Distilled water
culture temp
- @ref: 1955
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.872 |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_6823.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_524;96_3215;97_3945;98_5028;99_6823&stattab=map
- Last taxonomy: Thiothrix nivea subclade
- 16S sequence: HQ823668
- Sequence Identity:
- Total samples: 1448
- soil counts: 108
- aquatic counts: 1025
- animal counts: 245
- plant counts: 70
Safety information
risk assessment
- @ref: 1955
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thiothrix nivea (JP2) 16S rRNA sequence | M79435 | 323 | ena | 870187 |
| 20218 | Thiothrix nivea (JP2) 16S rRNA sequence | M79436 | 287 | ena | 870187 |
| 20218 | Thiothrix nivea (JP2) 16S rRNA sequence | M79437 | 421 | ena | 870187 |
| 20218 | Thiothrix nivea DSM 5205 16S ribosomal RNA gene, partial sequence | HQ823668 | 1399 | ena | 870187 |
| 20218 | Thiothrix nivea 16S ribosomal RNA (16S rRNA) gene, partial sequence | L40993 | 1427 | ena | 870187 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thiothrix nivea DSM 5205 | GCA_000260135 | scaffold | ncbi | 870187 |
| 66792 | Thiothrix nivea DSM 5205 | 870187.4 | wgs | patric | 870187 |
| 66792 | Thiothrix nivea JP2, DSM 5205 | 2506520049 | draft | img | 870187 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 72.783 | no |
| flagellated | no | 80.494 | no |
| gram-positive | no | 99.329 | no |
| anaerobic | no | 90.769 | no |
| aerobic | no | 50 | no |
| halophile | no | 90.558 | no |
| spore-forming | no | 90.816 | no |
| glucose-util | yes | 60.054 | no |
| glucose-ferment | no | 87.868 | no |
| thermophile | no | 98.808 | no |
External links
@ref: 1955
culture collection no.: DSM 5205, ATCC 35100
straininfo link
- @ref: 86079
- straininfo: 47903
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1955 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5205) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5205 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 86079 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47903.1 | StrainInfo: A central database for resolving microbial strain identifiers |